We use the R package pointblank
to review and validate the demographic data set
(HDP_1997_2009.csv) and plot-level descriptors
(HDP_plots.csv) published in Bruna et al. (2023) and
archived in the Dryad online data repository. The report below
includes:
Tests to determine if columns are correctly coded as integer,
character, etc.
Test criteria: Strict (‘stop’ if any rows
fail).
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Height is measured to nearest cm
|
— |
|
✓ |
57K |
57K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 2 | Shoots is interger
|
— |
|
✓ |
57K |
57K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 3 | Number of inflorescences is integer
|
— |
|
✓ |
2K |
2K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 2023-05-26 15:38:08 UTC < 1 s 2023-05-26 15:38:08 UTC | |||||||||||||
Test for any nonexistent values of plot_id (e.g.,
‘FF-10’, ‘CF-23’) or subplot (e.g., ‘H23’, ‘A11’).
Test criteria: Strict (‘stop’ if any rows
fail).
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | col_vals_in_set()
|
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | |||
| 2 | col_vals_in_set()
|
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | |||
| 2023-05-26 15:38:09 UTC < 1 s 2023-05-26 15:38:09 UTC | |||||||||||||
Tests for duplicated rows, missing plant_ID numbers, or
duplicate plant_id numbers (test is done for every survey
year).
Test criteria: Strict (‘stop’ if any rows
fail).
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | duplicated rows
|
— | — |
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | |
| 2 | col_vals_not_null()
|
— |
|
✓ |
67K |
67K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 3 | Check for duplicate ID's within each year
|
— |
|
✓ |
3K |
3K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 4 | Check for duplicate ID's within each year
|
— |
|
✓ |
4K |
4K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 5 | Check for duplicate ID's within each year
|
— |
|
✓ |
5K |
5K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 6 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 7 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 8 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 9 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 10 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 11 | Check for duplicate ID's within each year
|
— |
|
✓ |
7K |
7K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 12 | Check for duplicate ID's within each year
|
— |
|
✓ |
5K |
5K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 13 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 14 | Check for duplicate ID's within each year
|
— |
|
✓ |
6K |
6K1.00 |
00.00 |
— |
○ |
— |
— | ||
| 2023-05-26 15:38:10 UTC 2.4 s 2023-05-26 15:38:12 UTC | |||||||||||||
Tests to determine how many values of plant size (shts,
ht) or infloresence number (infl) are outside
the range of most values.
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if
\(\geq\) 2% of rows fail
conditions.
| Pointblank Validation | |||||||||||||
| Data Validation
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | shoots between 0 and 20
|
|
✓ |
67K |
67K0.99 |
80.01 |
● |
○ |
— |
||||
| 2 | height between 0 and 200cm
|
|
✓ |
67K |
67K0.99 |
20.01 |
● |
○ |
— |
||||
| 3 | infloresences between 0 and 3
|
|
✓ |
67K |
67K0.99 |
150.01 |
● |
○ |
— |
||||
| 2023-05-26 15:38:13 UTC < 1 s 2023-05-26 15:38:13 UTC | |||||||||||||
Tests for unusual changes in plant size from \[Year_{t}\] to \[Year_{t+1}\]. Conducted for both height and shoot number. Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if \(\geq\) 2% of rows fail conditions.
| Pointblank Validation | |||||||||||||
| Check growth & regression
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |% change in height| < 200%
|
|
✓ |
67K |
66K0.99 |
4200.01 |
● |
○ |
— |
||||
| 2 | |∆ height| < 100cm
|
|
✓ |
67K |
67K0.99 |
110.01 |
— |
● |
— |
||||
| 3 | |∆ shoot number| < 5
|
|
✓ |
67K |
67K0.99 |
2010.01 |
— |
● |
— |
||||
| 2023-05-26 15:38:14 UTC < 1 s 2023-05-26 15:38:14 UTC | |||||||||||||
Tests for seedlings whose size at initial marking was unusually
large. Conducted for both height and shoot number.
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if
\(\geq\) 2% of rows fail
conditions.
| Pointblank Validation | |||||||||||||
| Check seedlings
tibbleWARN
1
STOP
0.02
NOTIFY
—
|
|||||||||||||
| STEP | COLUMNS | VALUES | TBL | EVAL | UNITS | PASS | FAIL | W | S | N | EXT | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | shoots < 3
|
|
✓ |
3K |
3K0.99 |
120.01 |
● |
○ |
— |
||||
| 2 | height < 30cm
|
|
✓ |
3K |
3K0.99 |
30.01 |
● |
○ |
— |
||||
| 2023-05-26 15:38:15 UTC < 1 s 2023-05-26 15:38:15 UTC | |||||||||||||